Objective To investigate the changes in the anatomical structure of the lower renal calyx after the treatment of 2-3 cm lower renal calyx stones with improved tubeless percutaneous nephrolithotripsy（PCNL） and impact on postoperative stone clearance rate. Methods A total of 300 patients with 2-3 cm lower renal calyx stones admitted to the Department of Urology，Affiliated Hospital of Southwest Medical University between September 2020 and September 2023 were selected as the study subjects. After improved tubeless PCNL treatment，the patients were divided into clearance group（n=253） and non-clearance group（n=47）. Univariate analysis was performed on the general information of two groups of patients. The restricted cubic spline regression method was used to analyze the relationships between changes in anatomical parameters of the lower renal calyx and postoperative stone residue. Stepwise logistic regression was conducted to analyze influencing factors. Based on this，a nomogram prediction model was constructed. The receiver operating characteristic curve and calibration curve were drawn to evaluate model diagnostic effectiveness. Results There were significant differences between the two groups in history of renal dysfunction（P=0.017），infundibular length（P<0.001），number of stones（P=0.025），CT value of stones（P=0.001），infundibular width（P<0.001），surgical time（P=0.002），infundibulopelvic angle（P<0.001），pelvic calyceal height（P<0.001），uric acid（P<0.001），and blood urea nitrogen（P=0.014）. Logistic regression showed that adjusted infundibular length，pelvic calyceal height，infundibular width，and infundibulopelvic angle were still risk factors for postoperative stone residue. The results of stepwise logistic regression showed that the number of stones，CT value of stones，infundibular length，and pelvic calyceal height were independent risk factors affecting lower renal calyx stone residue in patients treated with improved tubeless PCNL，while infundibular width and infundibulopelvic angle were protective factors（P<0.05）. The influencing factors mentioned above were used to construct a nomogram prediction model. The regression equation was：Logit（P）=-2.567+0.110 9×X₁+1.170×X₂-0.226×X₃+0.023×X₄-0.442×X₅+0.714×X₆，with a consistency index of 0.893（95%CI=0.878-0.901）. The receiver operating characteristic curve showed that the area under the curve was 0.888（95%CI=0.869-0.897），the sensitivity was 0.827，and the specificity was 0.795，indicating high discrimination ability. The calibration curve indicated that the model had high accuracy. Conclusion Improved tubeless PCNL is a safe and effective method for the treatment of 2-3 cm lower renal calyx stones. Patients with lower renal calyx stones should fully consider anatomical factors before formulating treatment plans，and targeted preventive measures should be taken in clinical practice to increase the stone clearance rate after PCNL surgery.